Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34766.32 
• Atom Count: 2192 
• Residue Count: 298 
• Unique protein chains: 1

3UMW

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-3(2H)-one

• DOI: 10.2210/pdb3UMW/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: cell-free protein synthesis


• Deposited: 2011-11-14 Released: 2012-10-03 
• Deposition Author(s): Parker, L.J., Handa, N., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 

Literature

Rational evolution of a novel type of potent and selective proviral integration site in Moloney murine leukemia virus kinase 1 (PIM1) inhibitor from a screening-hit compound.

Nakano, H., Saito, N., Parker, L.J., Tada, Y., Abe, M., Tsuganezawa, K., Yokoyama, S., Tanaka, A., Kojima, H., Okabe, T., Nagano, T.

(2012) J.Med.Chem. 55: 5151-5164

• PubMed: 22540945 
• DOI: 10.1021/jm3001289


• PubMed Abstract: 
  

Serine/threonine kinase PIM1 is an emerging therapeutic target for hematopoietic and prostate cancer therapy. To develop a novel PIM1 inhibitor, we focused on 1, a metabolically labile, nonselective kinase inhibitor discovered in our previous screening study. We adopted a rational optimization strategy based mainly on structural information for the PIM1-1 complex to improve the potency and selectivity. This approach afforded the potent and metabolically stable PIM1-selective inhibitor 14, which shows only a marginal increase in molecular weight compared with 1 but has a significantly decreased cLogP. The validity of our design concept was confirmed by X-ray structure analysis. In a cellular study, 14 potently inhibited the growth of human leukemia cell line MV4-11 but had a negligible effect on the growth of WI-38 (surrogate for general toxicity). These results demonstrate the effectiveness of our design strategy for evolving the screening-hit compound 1 into a novel type of PIM1 inhibitor, 14.

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Organizational Affiliation: 

Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Proto-oncogene serine/threonine-protein kinase pim-1	A	298	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens) Go to Gene View: PIM1 Go to UniProtKB:  P11309

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
596	A	(2Z)-2-(1H-indazol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3(2H)-one C22 H22 N4 O3 HZMQZYRYZGLOKJ-NDENLUEZSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
596	IC50: 3 - 6 nM (100) BINDINGDB
596	IC50: 3 nM BINDINGMOAD
596	IC50: 3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 98.280	α = 90.00
b = 98.280	β = 90.00
c = 80.641	γ = 120.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-14 
• Released Date: 2012-10-03 
• Deposition Author(s): Parker, L.J., Handa, N., Yokoyama, S.

Revision History 

• Version 1.0: 2012-10-03
  Type: Initial release